In-game head canon

[King Feraligatr]

Back when I was younger, I'd have a tendency to try and connect some NPCs to my custom Pokemon villains. I'd also try to figure out who'd be actual members of the organization and who where just pawns. And since their ultimate goal is world domination, I'd try to come up with things to connect game events to their plans.

"Whole lotta stuff"

I also try to connect humanity's and Pokemon's connections to each other with my villains so they can make "superhumans"... people who can fight off Pokemon and just be more more durable and powerful while having none of the weaknesses of a Pokemon (being able to be caught, not being dominant, etc.). They're a human supremacist organization that exploits Pokemon and has the party line of only seeing them as tools, slaves, and test subjects. They're... uh... not good people.

 

[ScraftyIsTheBest]

For the Gen 5 games, I think both Black/2 and White/2 can be seen as canon... but only with the correct protagonists! I think Hilbert and Nate should be the protagonists for Black and Black 2, while Hilda and Rosa should be the protagonists for White and White 2. I guess the reason for this is because that was how I played my Gen 5 games, so I will always see it like this. If anyone plays Black/2 as the girl or White/2 as the boy, it goes completely against my headcanon in every possible way and I can't help but consider it wrong.

I think with regards to the "correct" protagonist with every game, I think the way you laid it out for the Gen 5 games can actually be sort of expanded so that both player characters of every region can be the protag, but for a different version. Like the "boy" protag is the canon protagonist for the A version, and the "girl" protag is the protagonist of the B version. With the exception of Gen 1 (only Red) and Gen 2 (Gold/Ethan is feasibly the protag of GS, but Kris can be interpreted as Crystal's protagonist). Something like this:

RBGY: Red
GS: Ethan, Crystal: Kris
Ruby: Brendan
Sapphire: May
FireRed: Red
LeafGreen: Leaf
Diamond: Lucas
Pearl: Dawn
HeartGold: Ethan
SoulSilver: Lyra
Black: Hilbert
White: Hilda
Black 2: Nate
White 2: Rosa
X: Calem
Y: Serena
Omega Ruby: Brendan
Alpha Sapphire: May
Sun/Ultra Sun: Elio
Moon/Ultra Moon: Selene
Let's Go, Pikachu!: Chase
Let's Go, Eevee!: Elaine
Sword: Victor
Shield: Gloria
Brilliant Diamond: Lucas
Shining Pearl: Dawn

Something like that. Many of the protags' color schemes even match the respective color schemes I laid out here, for example, with XY: Calem's default outfit is blue (befitting X's blue color scheme), and Serena's default outfit is dominantly red (befitting Y's red color scheme), or with DP/BDSP in which Lucas has traces of blue color scheme in his outfit while Dawn's stands out as pink.

Or in the case of SM/USUM, where the names reflect the games respectively. The boy protag's "name" is Elio, which draws from "helios" which is the God of the Sun in Greek mythology, while the girl protag's name is Selene, derived from the Goddess of the Moon in Greek mythology, hence Sun and Moon respectively making Elio the Sun/Ultra Sun protag while Selene is the Moon/Ultra Moon protag. Going into BDSP, the remake names are from the respective protag's Japanese names (Kouki and Hikari). Additionally, Kris's name is clearly from Crystal, for instance.

In some cases it's even more clearly implied, like in ORAS where in the respective openings: in Omega Ruby's opening you see Brendan, whereas in Alpha Sapphire's opening you see May.

Or in LGPE, where Chase, the boy protag, is dominantly seen with Pikachu, while Elaine, the girl protag, is dominantly seen with Eevee in marketing.

Now granted, this only applies well to games that are paired. In solitary games that aren't Crystal, such as Emerald, Platinum, and Legends: Arceus, this is more open to interpretation as there is only one continuity that can be interpreted as a singular canon in these instances. Though if we go by manga canon "Dawn" could feasibly be canon to Platinum, but that's still left open to interpretation. Emerald is very much either way. Meanwhile with the likes of Legends it can really go either way as to whether Rei or Akari are the "correct" protagonist.

Just a bit of a thought dump in this regard.

 

[Wukong]

I'll start with the BW protagonists and N first. We're told in the mythology that after two original brothers ceased their fight their sons renewed the quarrel a generation later, which led to both dragons disappearing. Now, generations later, my thinking is that Hilbert/Hilda and N are the (possibly direct) descendants of the two brothers, which would make them very distantly related.

This was something I read a lot during the early days of BW, so it's not even a theory I outright invented. My copy of Black is in Japanese and I don't have a copy of White so I can't replay to be sure, but I'm 99% certain nothing in the games ever directly states this. Regardless, it could still be true and doesn't ever even really need to be outright confirmed. It doesn't really add anything to the plot beyond thematic symbolism and a touch of fate, but I like the idea and it's more meaningful this way IMO. Of course, bloodline shouldn't be a prerequisite for who can raise a Pokemon, but it is frequently an important plot point in high fantasy, and what with the high fantasy vibes Unova has going on it feels quite natural. It does bring a sense of closure and relevance to the story to have the descendants of the brothers (hopefully) finally end the conflict between the Unova dragons.

I head canon this too actually. I like to imagine N and the BW protagonist as cousins because their fates just seem so conveniently intertwined with one another. I know this is perhaps an overdone high fantasy trope but it's just too ripe for the taking. While there's nothing in the games that even remotely insinuates this, there's also nothing that outright rejects this theory either, so I think it's fair game to head canon.

Interestingly, I chose Tepig when I played through Black 2. The reason being that I had picked Snivy in Black and Oshawott in White, so Tepig was obviously next in line. I agree with you that it works very well for the three main characters this way. I rarely ever think about "canon starters" but this was a very interesting point.

I also don't usually canon starters as I find most starters can be interchangeable as far as fitting protagonists and rivals. However, there's one exception: I have a difficult time wrapping my head around Silver with Chikorita in the Johto games. It just doesn't fit at all to be honest. Which is too bad because I quite often pick Totodile in HGSS. Maybe someone else has thoughts to rationalize this because I can't quite figure it out.

 

[Bakugames]

Maybe someone else has thoughts to rationalize this because I can't quite figure it out

Chikoritas evolution line has a more peaceful and friendly aspect, which means you could be having some dissonance as silver' pokemon tend to be either emotionless or look "evil" and "mean". While totodile and cyndaquil are very baby, they're easier to view as aggressive, and their evolution lines reinforce this

 

[Wukong]

Chikoritas evolution line has a more peaceful and friendly aspect, which means you could be having some dissonance as silver' pokemon tend to be either emotionless or look "evil" and "mean". While totodile and cyndaquil are very baby, they're easier to view as aggressive, and their evolution lines reinforce this

Yeah I understood that. But maybe somebody has a theory to rationalize why he chooses Chikorita in the scenario that you choose Totodile.

I read somewhere that the aroma Chikorita releases from its leaf is supposed to have a calming effect. Which might explain why Silver who lived a troubled life with his father abandoning him might gravitate towards it. But that's all I can think of.

 

[Bakugames]

Yeah I understood that. But maybe somebody has a theory to rationalize why he chooses Chikorita in the scenario that you choose Totodile.

You could go two ways I think:

He's watching from the window, so I think he sees your choice and picks whichever seems stronger against you because he thinks your choice sucks.
Or he picks a pokéball at random after the pokémon was already put back, which leads to the game just doing "it's always the one stronger than you"